Overview

This report summarizes the results of the immune analysis module, which runs several algorithms assigning immune scores for understanding the tumor microenvironment. Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE, Yoshihara et al., 2013) uses gene expression signatures to calculate the fraction of stromal and immune cells and infer tumor purity. xCell (Aran et al., 2017) uses a gene signature-based method to infer immune and stromal cell types. ImmuneSubtypeClassifier (Thorrson et al., 2018) uses immune gene expression signatures to classify tumor samples into one of 6 immune subtypes. Enrichment analysis (Fisher’s exact test) is performed on immune subtypes and significant results at p-value < 0.05 reported. Documentation for the immune analysis module can be found here.

xCell scores

Figure: Heatmap showing xCell scores for each sample. Rows (cell types) and columns (samples) are clustered by hierarchical clustering using the Pearson correlation method. Sample annotations, including key immune scores from all three algorithms, are labeled at the top of the heatmap.

Comparison of xCell and ESTIMATE scores

Figure: Interactive scatter plots comparing Immune and Stromal Scores calculated by xCell and ESTIMATE. Hovering over each point reveals which sample it corresponds to.

Immune subtype enrichment analysis

Number of significant enrichments between immune subtypes and annotation groups: 0